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Dog Doo Afternoon: Researchers Sort Fecal Samples for Science

Science can be so glamorous: Groundbreaking research with life-changing results! And then there’s sorting frozen dog poop. Members of the Hendricks Lab spent part of their holiday break in the basement freezer room at TGen cataloguing frozen boxes filled with tiny plastic tubes of canine blood, stomach contents and excrement.

Science can be so glamorous: Groundbreaking research with life-changing results!

And then there’s sorting frozen dog poop.

Members of the Hendricks Lab spent part of their holiday break in the basement freezer room at TGen cataloguing frozen boxes filled with tiny plastic tubes of canine blood, stomach contents and excrement.

“This a project we called ‘poop to prediction’ where we’re sequencing the DNA from poop to look for biomarkers of disease in the gut flora of dogs,” explained lab manager Tory Zismann. “This is part of our microbiome work.”

Before that work — or any work — can be done, the samples must be coded and inventoried so they can be tracked through our workflows. TGen Assistant Professor Jonathan Keats, our Director of Bioinformatics, developed a program called KBase that helps our researchers keep track of the samples that come through TGen.

"In a place like TGen we are fortunate to have patients provide precious samples for which we really can not associate a value because they are invaluable," explained Dr. Keats.  "All too often, these precious samples can be lost, illegibly labelled, or forgotten about in the depths of freezers.  To ensure every sample and every resulting test result are never lost, we built KBase to track who things came from, where these things are, and where the results for each test are stored on our computers. It even allows researchers to initiate analysis of samples though our analysis pipelines with a single click of a button."

To date, the Collaborative Sequencing Center at TGen has sequenced close to 25,000 DNA and RNA samples — and that doesn’t count biofluids and tissues analyzed by the Collaborative Center for Translational Mass Spectrometry. 

Unlike human tissue, canine samples do not have to be de-identified. Tiny vials of the stomach contents donated from Buster, Zena, Racer and other four-legged friends are being used to study a condition called gastric dilatation-volvulus, also known as “bloat” or “twisted stomach” to see if certain breeds have a genetic predisposition to the condition.

The tissue samples are donated by pet parents, veterinarians and academic collaborators — dogs are not housed for research purposes — and they are stored in the industrial freezers while they await sequencing. Research associate Salvatore Facista organized the afternoon expedition to clear a backlog of canine samples.

“This one is from April 2017, so it’s pretty fresh,” said Facista, as he placed a box of test tubes into dry ice so he could maintain the sub-zero temperature of the samples while he worked. Between the banks of freezers, research associate Shukmei Wong and intern Yasmine Mian worked through their own boxes of tubes. All totalled, the Hendricks Lab inventoried more than 1,300 samples from 400 canine patients.

So if you’re looking for a cool place to hang out, the basement at TGen is where it’s at… if you don’t mind the dog poop.

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